An optimized ultra-deep massively parallel sequencing with unique molecular identifier tagging for detection and quantification of circulating tumor DNA from lung cancer patients.

Authors

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Hong-Anh Thi Pham

Gene Solutions, Vietnam, Medical Genetics Institute, Vietnam, Graduate Program of Genetics, Ho Chi Minh City University of Science, Ho Chi Minh, Viet Nam

Hong-Anh Thi Pham , Le Son Tran , Uyen Vu Tran , Thanh-Truong Tran , Hoai-Nghia Nguyen , Hoa Giang , Anh-Thu Huynh Dang , Dinh-Thong Vu Le , Son-Lam Vu Nguyen , Ngoc-Vu Vu Nguyen , Vu Trieu Nguyen , Binh Thanh Vo , Nguyen Huu Nguyen , Chu Van Nguyen , Cam Phuong Pham , Anh Tuan Dang-Mai , Thien Kim Dinh-Nguyen , Van Hieu Phan , Thuy Thanh Do , Kiet Truong Dinh

Organizations

Gene Solutions, Vietnam, Medical Genetics Institute, Vietnam, Graduate Program of Genetics, Ho Chi Minh City University of Science, Ho Chi Minh, Viet Nam, Medical Genetics Institute, Ho Chi Minh City, Viet Nam, Gene Solutions, Vietnam, Medical Genetics Institute, Ho Chi Minh City, Vietnam, Graduate Program of Genetics, Ho Chi Minh City University of Science, Ho Chi Minh, Viet Nam, Gene Solutions, Vietnam, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh, Viet Nam, Gene Solutions, Vietnam; Medical Genetics Institute, Ho Chi Minh City, Vietnam, Ho Chi Minh, Viet Nam, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh, Viet Nam, Pham Ngoc Thach Hospital, Ho Chi Minh, Viet Nam, Thu Duc Hospital, Ho Chi Minh City, Vietnam, Gene Solutions, Vietnam, Ho Chi Minh, Viet Nam, National K Cancer Hospital, Ha Noi, Viet Nam, Bach Mai Hospital, Hanoi, Viet Nam, Forensic Center, Ho Chi Minh, Viet Nam, Tan Hung General Hospital, Ho Chi Minh, Viet Nam, Medical Genetics Institute, Ho Chi Minh, Viet Nam

Research Funding

Pharmaceutical/Biotech Company
Vietnam National Foundation for Science and Technology Development (NAFOSTED), Ho Chi Minh City Department of Science, Gene Solutions.

Background: The identification and quantification of actionable mutations are of critical importance for effective genotype-directed therapies, prognosis and drug response monitoring in patients with non-small-cell lung cancer (NSCLC). Although tumor tissue biopsy remains the gold standard for diagnosis of NSCLC, the analysis of plasma circulating tumor DNA (ctDNA), known as liquid biopsy, has recently emerged as an alternative and noninvasive approach for exploring tumor genetic constitution. In this study, we developed a mutation detection approach for liquid biopsy using ultra-deep massively parallel sequencing (MPS) with unique molecular identifier (UID) tagging and evaluated its performance for the identification and quantification of tumor-derived mutations from plasma of patients with advanced NSCLC. Methods: Tissue biopsy and plasma samples were collected from a total of 58 patients diagnosed with NSCLC in Vietnam. Genetic alterations in four driver genes including EGFR, KRAS, NRAS and BRAF were identified by using ultra-deep MPS combined with UID tagging. Subsequently, the concordance rate of mutation testing between matched plasma and tissue samples was assessed. Additionally, a commercially available ddPCR (Bio-rad) assay was used to conduct a cross-platform comparison with ultra-deep MPS for the detection and quantification of the three most common actionable EGFR mutations (del19, L858R and T790M). Results: Compared to the mutations detected in paired tissue samples, the plasma based ultra-deep MPS achieved high concordance rate of 87.5%. Cross-platform comparison with droplet digital PCR demonstrated comparable detection performance (91.4% concordance, Cohen's kappa coefficient of 0.85 with 95% CI = 0.72 – 0.97) and great reliability in quantification of mutation allele frequency (Intraclass correlation coefficient of 0.96 with 95% CI = 0.90 – 0.98). Conclusions: Our results highlight the potential application of liquid biopsy using ultra-deep MPS as a routine assay in clinical practice for both detection and quantification of actionable mutation landscape in NSCLC patients.

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Abstract Details

Meeting

2019 Breakthrough

Session Type

Poster Session

Session Title

Poster Session A: Access to Care, Diagnostics, Early Detection and Diagnosis, Prevention and Screening, and Surveillance

Track

Access to Care,Diagnostics,Early Detection and Diagnosis,Prevention and Screening,Surveillance

Sub Track

Early Detection and Diagnosis

Citation

J Glob Oncol 5, 2019 (suppl 1; abstr 55)

DOI

10.1200/JGO.2019.5.suppl.55

Abstract #

55

Poster Bd #

D9

Abstract Disclosures